Kinetics of Formation and Oxidation of 8-oxo-7,8-dihydroguanine (8oxoG)

8-oxo-7,8-dihydroguanine (8oxoG) is one of the most important base lesions formed during oxidative damage of DNA. The aim of the present research was to investigate the effects of DNA concentration, G content, and the nature of oxidizing species on the kinetics of 8oxoG in model DNA solutions by using HPLC. The experimentally obtained yields of 8oxoG were typically in the range of 2-2.5% of total concentration of guanine. The ratios of the rate constant of hole diffusion in DNA to the rate constant of conversion of the hole into 8oxoG (kd/kr) were calculated from the experimental data using the diffusion model of charge transfer in DNA to be in the range of 200-300, in agreement with previously reported kd/kr ratios in the duplex DNA oligonucleotides (GGA)n or (GGTT)n. Our current diffusion model cannot satisfactorily explain the absence of the G content dependence of the 8oxoG yields, which indicates that a more advanced model is required

PROBING VIBRATIONAL WAVE PACKETS IN ORGANOPHOSHOROUS MOLECULES USING FEMTOSECOND TIME-RESOLVED MASS SPECTROMETRY

Organic phosphates and phosphonates share a basic structure with organophoshorous chemical warfare agents and cellular components such as DNA. To understand ultrafast nuclear dynamics in isolated organic phosphates and phosphonates, Femtosecond Time Resolved Mass Spectrometry (FTRMS) was employed. FTRMS applies the pump-probe technique with mass spectrometric detection. In our experiment an ionizing $10^{14}$ W cm$^{-2}$, 1500 nm, 18 fs pump and a non-ionizing $10^{13}$ W cm$^{-2}$, 800 nm, 25 fs probe pulse were used. Experiments were performed on four related compounds: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), diisopropyl methylphosphonate (DIMP) and trimethyl phosphate (TMP). The yields of parent molecular ions generated by the pump pulse exhibited ultrafast oscillations with the period depending on the parent molecule. These oscillations indicate the presence of a vibrational wave packet that is excited upon ionization. In DMMP, a well resolved peak of 45 fs ($732\pm28$ cm$^{-1}$) was observed with a weak feature at 610-650 cm$^{-1}$, while DIMP exhibits bimodal oscillation with frequencies of $554\pm28$ and 670-720 cm$^{-1}$. Oscillations for DEMP were barely visible due to rapid decay. The high- and low- frequency oscillations in DMMP and DIMP were assigned to coherent excitation of O-P-O bend and P-C stretching respectively based on DFT calculations. Bimodal oscillations at 770 and 880 cm$^{-1}$ in TMP were also observed and are tentatively assigned to the symmetric and asymmetric P-O stretching modes. These results suggest that this group of compounds exhibits similar coherent vibrational excitation upon ionization. These results may have applications to development of new organophosphorous chemical warfare agent detection and destruction techniques based on the coherent control and may point to reaction pathways in organophosphorous compounds of biological relevance

Probing Coherent Vibrations of Organic Phosphonate Radical Cations with Femtosecond Time-Resolved Mass Spectrometry

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs (732 ± 28 cm−1) oscillations with a weak feature at 610–650 cm−1, while DIMP exhibits bimodal oscillations with a period of ∼55 fs and two frequency features at 554 ± 28 and 670–720 cm−1. In contrast, the oscillations in DEMP decay too rapidly for effective resolution. The low- and high-frequency oscillations in DMMP and DIMP are assigned to coherent excitation of the symmetric O–P–O bend and P–C stretch, respectively. The observation of the same ionization-induced coherently excited vibrations in related molecules suggests a possible common excitation pathway in ionized organophosphorus compounds of biological relevance, while the distinct oscillatory dynamics in each molecule points to the potential use of FTRMS to distinguish among fragment ions produced by related molecules

Probing Coherent Vibrations of Organic Phosphonate Radical Cations with Femtosecond Time-Resolved Mass Spectrometry

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs (732 ± 28 cm−1) oscillations with a weak feature at 610–650 cm−1, while DIMP exhibits bimodal oscillations with a period of ∼55 fs and two frequency features at 554 ± 28 and 670–720 cm−1. In contrast, the oscillations in DEMP decay too rapidly for effective resolution. The low- and high-frequency oscillations in DMMP and DIMP are assigned to coherent excitation of the symmetric O–P–O bend and P–C stretch, respectively. The observation of the same ionization-induced coherently excited vibrations in related molecules suggests a possible common excitation pathway in ionized organophosphorus compounds of biological relevance, while the distinct oscillatory dynamics in each molecule points to the potential use of FTRMS to distinguish among fragment ions produced by related molecules

Conserved Vibrational Coherence in the Ultrafast Rearrangement of 2-Nitrotoluene Radical Cation

2-Nitrotoluene (2-NT) is a good model for both photolabile protecting groups for organic synthesis and the military explosive 2,4,6-trinitrotoluene (TNT). In addition to the direct C−NO2 bond-cleavage reaction that initiates detonation in TNT, 2-NT undergoes an H atom attack reaction common to the photolabile 2-nitrobenzyl group, which forms the aci-nitro tautomer. In this work, femtosecond pump−probe measure- ments with mass spectrometric detection and density functional theory (DFT) calculations demonstrate that the initially prepared vibrational coherence in the 2-NT radical cation (2- NT+) is preserved following H atom attack. Strong-field adiabatic ionization is used to prepare 2-NT+, which can overcome a modest 0.76 eV energy barrier to H atom attack to form the aci-nitro tautomer as soon as ∼20−60 fs after ionization. Once formed, the aci-nitro tautomer spontaneously loses −OH to form C7H6NO+, which exhibits distinctly faster oscillations in its ion yield (290 fs period) as compared to the 2-NT+ ion (380 fs period). The fast oscillations are attributed to the coherent torsional motion of the aci-nitro tautomer, which has a significantly faster computed torsional frequency (86.9 cm−1) than the 2- NT+ ion (47.9 cm−1). Additional DFT calculations identify reaction pathways leading to the formation of the dissociation products C7H6NO+, C7H7+, and C6H6N+. Collectively, these results reveal a rich picture of coherently and incoherently driven dissociation pathways in 2-NT+

Dissociation of Singly and Multiply Charged Nitromethane Cations: Femtosecond Laser Mass Spectrometry and Theoretical Modeling

Dissociation pathways of singly- and multiply charged gas-phase nitromethane cations were investigated with strong-field laser photoionization mass spectrometry and density functional theory computations. There are multiple isomers of the singly charged nitromethane radical cation, several of which can be accessed by rearrangement of the parent CH3–NO2 structure with low energy barriers. While direct cleavage of the C–N bond from the parent nitromethane cation produces NO2+ and CH3+, rearrangement prior to dissociation accounts for fragmentation products including NO+, CH2OH+, and CH2NO+. Extensive Coulomb explosion in fragment ions observed at high laser intensity indicates that rapid dissociation of multiply charged nitromethane cations produces additional species such as CH2+, H+, and NO22+.  On the basis of analysis of Coulomb explosion in the mass spectral signals and pathway calculations, sufficiently intense laser fields can remove four or more electrons from nitromethane

From Neutral Aniline to Aniline Trication: A Computational and Experimental Study

We report density functional theory computations and photoionization mass spectrometry measurements of aniline and its positively charged ions. The geometrical structures and properties of the neutral, singly, doubly, and triply positively charged aniline are computed using density functional theory with the generalized gradient approximation. At each charge, there are multiple isomers closely spaced in total energy. Whereas the lowest energy states of both neutral and cation have the same topology C6H5–NH2, the dication and trication have the C5NH5–CH2 topology with the nitrogen atom in the meta and para positions, respectively. We compute the dissociation pathways of all four charge states to NH or NH+ and NH2 or NH2+, depending on the initial charge of the aniline precursor. Dissociation leading to the formation of NH (from the neutral and cation) and NH+ (from the dication and trication) proceeds through multiple transition states. On the contrary, the dissociation of NH2 (from the neutral, cation) and NH2+ (from the dication and trication) is found to proceed without an activation energy barrier. The trication was found to be stable toward abstraction on NH+ and NH2+by 0.96 eV and 0.18 eV, respectively, whereas the proton affinity of the trication is substantially higher, 1.98 eV. The mass spectra of aniline were recorded with 1300 nm, 20 fs pulses over the peak intensity range of 1 x 1013 W cm-2 to 3 x 1014W cm-2. The analysis of the mass spectra suggests high stability of both dication and trication to fragmentation. The formation of the fragment NH+ and NH2+ ions is found to proceed via Coulomb explosion

Ultrafast Dynamics of Nitro−Nitrite Rearrangement and Dissociation in Nitromethane Cation

We report new insights into the ultrafast rearrange- ment and dissociation dynamics of nitromethane cation (NM+) using pump−probe measurements, electronic structure calculations, and ab initio molecular dynamics simulations. The “roaming” nitro−nitrite rearrangement (NNR) pathway involving large- amplitude atomic motion, which has been previously described for neutral nitromethane, is demonstrated for NM+. Excess energy resulting from initial population of the electronically excited D2 state of NM+ upon strong-field ionization provides the necessary energy to initiate NNR and subsequent dissociation into NO+. Both pump−probe measurements and molecular dynamics simulations are consistent with the completion of NNR within 500 fs of ionization with dissociation into NO+ and OCH3 occurring ∼30 fs later. Pump−probe measurements indicate that NO+ formation is in competition with the direct dissociation of NM+ to CH3+ and NO2. Electronic structure calculations indicate that a strong D0 → D1 transition can be excited at 650 nm when the C−N bond is stretched from its equilibrium value (1.48 Å) to 1.88 Å. On the other hand, relaxation of the NM+ cation after ionization into D0 occurs in less than 50 fs and results in observation of intact NM+. Direct dissociation of the equilibrium NM+ to produce NO2+ and CH3 can be induced with 650 nm excitation via a weakly allowed D0 → D2 transition

DNA Damage by the Sulfate Radical Anion: Hydrogen Abstraction From the Sugar Moiety Versus One-Electron Oxidation of Guanine

The products of oxidative damage to double-stranded (ds) DNA initiated by photolytically generated sulfate radical anions SO4•− were analyzed using reverse-phase (RP) high-performance liquid chromatography (HPLC). Relative efficiencies of two major pathways were compared: production of 8-oxoguanine (8oxoG) and hydrogen abstraction from the DNA 2-deoxyribose moiety (dR) at C1,′ C4,′ and C5′ positions. The formation of 8oxoG was found to account for 87% of all quantified lesions at low illumination doses. The concentration of 8oxoG quickly reaches a steady state at about one 8oxoG per 100 base pairs due to further oxidation of its products. It was found that another guanine oxidation product identified as 2-amino-5-(2′-alkylamino)-4H-imidazol-4-one (X) was released in significant quantities from its tentative precursor 2-amino-5-[(2′-deoxy-β-d-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz) upon treatment with primary amines in neutral solutions. The linear dose dependence of X release points to the formation of dIz directly from guanine and not through oxidation of 8oxoG. The damage to dR was found to account for about 13% of the total damage, with majority of lesions (33%) originating from the C4′ oxidation. The contribution of C1′ oxidation also turned out to be significant (17% of all dR damages) despite of the steric problems associated with the abstraction of the C1′-hydrogen. However, no evidence of base-to-sugar free valence transfer as a possible alternative to direct hydrogen abstraction at C1′ was found